A new version of 3dsutils (the tool for dumping system archives) is available. It is compiled by me based on this branch: https://github.com/citra-emu/3dsutils/pull/15 (which is basically the same as the updated master branch except one additional flag to make it compile…).
This new version of 3dsutils only works for citra nightly build after e634b75 (currently the latest one), inclusive, and will also work for the next upcoming bleeding edge build. The old version of 3dsutils still works for all citra versions, but it is deprecated.
The system archive dumping guide is also updated accordingly